I have raw fastq files (forward, reverse, barcodes) from multiple seq runs (5 runs) with overlapping barcodes (EMP protocol). I was wondering, after importing data to QIIME2 and demultiplexing them by sampleIDs, is there anyway that I can combine the demultiplexed files and then use the combined file to analyze using DADA2 (following Atacama soil microbiome tutorial)? Can we convert multiple demultiplexed files to fastq format and combine them using cat and then continue from there? With new approaches (DADA2 and Deblur), is it possible/preferred to pick the sequence variants of samples belonging to each run separately and then merging the final tables? considering that down the road we are going to perform some analyses at the OTU (sequence) level, merging different tables seems to be impractical.
Appreciate your advice on this matter!